Research workbench
The SELENOMETHIONINE(SEMET)-derived CAS13D binary complex
Analyse The SELENOMETHIONINE(SEMET)-derived CAS13D binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IV8
- Type
- protein + RNA
- Length
- 1,835 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The selenomethionine (semet)-labeled CAS13D; RNA (51-mer); RNA (53-mer)
- UniProt
- A0A1C5SD84
- Ligands
- MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | The selenomethionine (semet)-labeled CAS13D | protein | 869 | 64% helix, 5% strand | A0A1C5SD84 |
| B | RNA (51-mer) | rna | 51 | — | — |
| D | RNA (53-mer) | rna | 53 | — | — |
| C | The selenomethionine (semet)-labeled CAS13D | protein | 862 | 64% helix, 5% strand | A0A1C5SD84 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.85 | 0.90 | 64 | empty |
| 2 | 607 | 0.83 | 0.89 | 83 | empty |
| 3 | 431 | 0.82 | 0.90 | 57 | empty |
| 4 | 277 | 0.79 | 0.91 | 35 | empty |
| 5 | 375 | 0.79 | 0.89 | 49 | empty |
Interfaces
3 interfaces between chains.
- D–C · 4556 Ų buried · 105 hydrogen bonds · protein-nucleic
- A–B · 4282 Ų buried · 106 hydrogen bonds · protein-nucleic
- A–C · 234 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 modified (engineered).
Compared structures
- 6IV8 · the selenomethionine(SeMet)-derived Cas13d binary complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A1C5SD84
- Elsewhere: RCSB PDB 6IV8 · PDBe 6IV8 · UniProt A0A1C5SD84
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